Changeset 9291d04 for src/Actions

Timestamp:

Feb 27, 2013, 12:42:36 PM (12 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

39a07a

Parents:

c7c615

git-author:

Frederik Heber <heber@…> (12/11/12 10:39:30)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:36)

Message:

Split saturation with hydrogen of treatment of hydrogen.

• now saturation means dangling bonds are saturated, and treatment means that in a bond graph hydrogen is skipped.
• FragmentationAction and DepthFirstSearchAction adapted in options.

Location:

src/Actions

Files:

• FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)
• FragmentationAction/FragmentationAction.def (modified) (1 diff)
• FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)
• GraphAction/DepthFirstSearchAction.cpp (modified) (1 diff)
• GraphAction/DepthFirstSearchAction.def (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -100 +100 @@
   }
 
-  // get whether to saturate or not
-  const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-
   // parse in Adjacency file
   boost::shared_ptr<AdjacencyList> FileChecker;
@@ -143 +140 @@
     LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
         << " atoms, out of " << mol->getAtomCount() << ".");
-    Fragmentation Fragmenter(mol, *FileChecker, saturation);
+    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    Fragmentation Fragmenter(mol, *FileChecker, treatment);
 
     // perform fragmentation
@@ -167 +165 @@
   // store molecule's fragment to file
   {
+    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
     ExportGraph_ToFiles exporter(TotalGraph, saturation);
     exporter.setPrefix(params.prefix.get());

src/Actions/FragmentationAction/FragmentationAction.def

@@ -20 +20 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(double)(unsigned int)(bool)(std::vector<std::string>)
-#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("output-types")
-#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("type(s) of parsers that output fragment config files")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true)) (PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
-#define paramreferences (prefix)(distance)(order)(DoSaturation)(types)
+#define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)
+#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")
+#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
+#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)
 #define paramvalids \
 (DummyValidator< std::string >()) \
 (BoxLengthValidator()) \
 (DummyValidator< unsigned int >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >()) \
 (STLVectorValidator< std::vector<std::string> >(1, 10, ParserTypeValidator()))

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -65 +65 @@
 #include "Fragmentation/ForceMatrix.hpp"
 #include "Fragmentation/Fragmentation.hpp"
-#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "Fragmentation/Homology/HomologyGraph.hpp"

src/Actions/GraphAction/DepthFirstSearchAction.cpp

@@ -71 +71 @@
       LocalBackEdgeStack = new std::deque<bond::ptr >; // no need to have it Subgraphs->Leaf->BondCount size
       DFS.PickLocalBackEdges(ListOfAtoms, LocalBackEdgeStack);
-      CyclicStructureAnalysis CycleAnalysis(params.DoSaturation.get() ? DoSaturate : DontSaturate);
+      CyclicStructureAnalysis CycleAnalysis(params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen);
       CycleAnalysis(LocalBackEdgeStack);
       delete(LocalBackEdgeStack);

src/Actions/GraphAction/DepthFirstSearchAction.def

@@ -15 +15 @@
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
 #define paramtypes (bool)
-#define paramtokens ("DoSaturate")
+#define paramtokens ("ExcludeHydrogen")
 #define paramdescriptions ("whether to treat hydrogen special or not")
 #define paramdefaults (PARAM_DEFAULT(true))
-#define paramreferences (DoSaturation)
+#define paramreferences (HowtoTreatHydrogen)
 #define paramvalids \
 (DummyValidator< bool >())